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Contribution Guide

We would love for you to contribute to the neurodamus project and help make it better than it is today. As a contributor, here are the guidelines we would like you to follow:

Got a Question?

Please do not hesitate to raise an issue on github project page.

Found a Bug?

If you find a bug in the source code, you can help us by submitting an issue to our GitHub Repository. Even better, you can submit a Pull Request with a fix.

Missing a Feature?

You can request a new feature by submitting an issue to our GitHub Repository. If you would like to implement a new feature, please submit an issue with a proposal for your work first, to be sure that we can use it.

Please consider what kind of change it is:

  • For a Major Feature, first open an issue and outline your proposal so that it can be discussed. This will also allow us to better coordinate our efforts, prevent duplication of work, and help you to craft the change so that it is successfully accepted into the project.
  • Small Features can be crafted and directly submitted as a Pull Request.

Submission Guidelines

Issues

Before you submit an issue, please search the issue tracker, maybe an issue for your problem already exists and the discussion might inform you of workarounds readily available.

We want to fix all the issues as soon as possible, but before fixing a bug we need to reproduce and confirm it. In order to reproduce bugs we will need as much information as possible, and preferably with an example.

Pull Requests

When you wish to contribute to the code base, please consider the following guidelines:

  • Make a fork of this repository.

  • Make your changes in your fork, in a new git branch:

    git checkout -b my-fix-branch master

  • Create your patch, including appropriate Python test cases. Please check the coding conventions for more information.

  • Run the full test suite, and ensure that all tests pass.

  • Commit your changes using a descriptive commit message.

    git commit -a

  • Push your branch to GitHub:

    git push origin my-fix-branch

  • In GitHub, send a Pull Request to the master branch of the upstream repository of the relevant component.

  • If we suggest changes then:

    • Make the required updates.

    • Re-run the test suites to ensure tests are still passing.

    • Rebase your branch and force push to your GitHub repository (this will update your Pull Request):

       git rebase master -i
 git push -f

That’s it! Thank you for your contribution!

After your pull request is merged

After your pull request is merged, you can safely delete your branch and pull the changes from the main (upstream) repository:

  • Delete the remote branch on GitHub either through the GitHub web UI or your local shell as follows:

    git push origin --delete my-fix-branch

  • Check out the master branch:

    git checkout master -f

  • Delete the local branch:

    git branch -D my-fix-branch

  • Update your master with the latest upstream version:

    git pull --ff upstream master

Development Environment

Please make sure to install the project requirements, see the dependencies section in top README.

This section applies to both Python versions 2 and 3.

Setup

It is recommended to use virtualenv to develop in a sandbox environment:

virtualenv venv
. venv/bin/activate

# Install neurodamus in development mode
pip install -e .

# Install test requirements
pip install -r tests/requirements.txt

Testing

There are several test groups in Neurodamus, from plain unit tests to integration and system tests.

While developing you may want to run unit tests very frequently and thus we suggest running the base tests using pytest directly from the dev environment.

pytest tests/unit

For the next stage testing we suggest using the provided tox environments

# Integration tests
tox -e integration

System and scientific tests require Blue Brain models. They therefore depend on neurodamus-neocortex special builds and should be launched as follows:

module load unstable neurodamus-neocortex py-neurodamus
# Integration-e2e tests
tox -e bbp-model -- tests/integration-e2e

# Scientific tests
tox -e bbp-model -- tests/scientific

Adding more tests

We kindly ask contributors to add tests alongside their new features or enhancements. With the previous setup in mind, consider adding test to one or more groups:

  • tests/unit: For unit tests of functions with little dependencies. Tests get a few shared mocks, namely for NEURON and MPI.
  • tests/integration: For integration tests. Please place here tests around a component which might depend on a number of functions. Tests here can rely on NEURON and the other base dependencies. Additionally tests are provided a special with synapse mechanisms so that Neurodamus can be fully initialized.
  • tests/integration-e2e: Place tests here that require launching a top-level Neurodamus instance. Examples of it might be testing modes of operation, parameter handling, or simply larger integration tests which are validated according to the results.
  • tests/scientific[-ngv]: Should contain tests which validate essential scientific features implemented in Neurodamus, namely creation of synapses, replay, NGV, neurodamulation, etc.

Coding conventions

The code coverage of the Python unit-tests may not decrease over time. It means that every change must go with their corresponding Python unit-tests to validate the library behavior as well as to demonstrate the API usage.